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2018-11-20correct sha for axl v1.1 (#9907)Elsa Gonsiorowski, PhD1-1/+1
2018-11-20package: add asciidoctor gem (#9905)Tom Scogland1-0/+20
* package: add asciidoctor gem Faster, easier to use, less impossible to install correctly implementation of asciidoc. * ritual sacrifice of EOF whitespace to flake8
2018-11-20CP2K related fixes and update (#9308)Tiziano Müller4-91/+205
* openblas: enable parallel builds * cp2k: enable parallel builds * cp2k: fix building on multilib/Suse distros use the actual directory path where files where installed to instead of the default prefix+'/lib' * cp2k: ensure we have a non-header-only libxsmm * openblas: disable max num CPU detection on virtualized build * cp2k: install data and set compiled-in DATA_DIR * cp2k: make libxc an optional dependency (enabled by default) * cp2k: link libint statically * cp2k: declare statically linked library deps as type=build * cp2k: add support for PGI compiler * cp2k: rename smm=none to smm=blas for clarification * cp2k: blacklist unsupported compilers * cp2k: mark wannier90 a build-time dep since statically linked * cp2k: make pexsi and elpa optional * cp2k: add support for v6.1 * libxc: add version 4.2.3 * cp2k: use pkg-config to link properly to libxsmm * cp2k: fix OpenMP support by making it explicit Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes being spawned even though no explicit OpenMP was requested. Now the `popt` variant should truly be thread free while the `psmp` variant uses threads also internally. * cp2k: source tarballs moved to GitHub
2018-11-20Package: Mercury (#9903)dorier1-0/+56
* added mercury package * updating mercury package to satisfy flake8 * improved mercury package
2018-11-20Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899)Jon Rood5-0/+17
* Add 2019.1 and 2018.4 version of the Intel performance libraries. * Fixing typo.
2018-11-19mpifileutils: add v0.8.1 (#9346)Adam Moody1-0/+1
2018-11-19openssl: make 1.1.1 the default version (#9836)Michael Kuhn1-3/+8
* openssl: add 1.0.2p, 1.1.0i and 1.1.1 * openssl: make 1.1.1 the default version
2018-11-19added several new perl modules (#9760)Justin Stanley17-0/+270
2018-11-19circos: new package starting at 0.69-6 (#9761)Justin Stanley1-0/+43
* circos: new package starting at 0.69-6 * circos: add homepage, simplify paths * circos: simplified more paths
2018-11-19gdk-pixbuf: explicitly disable building of gtk-docs (#9882)Sinan1-0/+11
2018-11-19r-rrpp: new package (#9887)Levi Baber1-0/+29
2018-11-19Adding openmpi version 4.0.0 (#9888)Jon Rood1-4/+5
2018-11-19breseq: Add version 0.33.1 (#9889)Eric1-0/+1
2018-11-19package/harfbuzz: disable building of gtk-docs, add new version (#9891)Sinan1-0/+12
2018-11-19r-crosstalk: remove unnecessary constraint (#9892)Levi Baber1-1/+0
2018-11-19r-geomorph: new version (#9890)Levi Baber1-0/+3
* r-geomorph: new version * r-geomorph: min r version
2018-11-19r-diversitree: new package (#9893)Levi Baber1-0/+33
* r-diversitree: new package * r-diversitree: system reqs
2018-11-19r-paleotree: new package (#9895)Levi Baber1-0/+24
2018-11-19package/pango: disable gtk-docs (#9896)Sinan1-0/+9
2018-11-19package/gtkplus: disable gtk-docs (#9897)Sinan1-0/+11
2018-11-19Explicitly set FC= empty for non-fortran builds (#9898)Mark C. Miller1-0/+2
2018-11-19Trimmomatic: Add version 0.38 (#9883)Eric1-0/+1
2018-11-19Adding intel-parallel-studio cluster 2019.1 version (#9884)Jon Rood1-0/+1
2018-11-19Add UCX v1.4.0 (#9881)Daniel Topa1-1/+3
Verification build dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5 ==> Installing libsigsegv ==> Installing m4 ==> Installing pkgconf ==> Installing ncurses ==> Installing readline ==> Installing gdbm ==> Installing perl ==> Installing autoconf ==> Installing automake ==> Installing libtool ==> Installing numactl ==> Installing zlib ==> Installing openssl ==> Installing diffutils ==> Installing bzip2 ==> Installing xz ==> Installing libxml2 ==> Installing tar ==> Installing gettext ==> Installing help2man ==> Installing bison ==> Installing flex ==> Installing libnl ==> Installing rdma-core ==> Installing ucx ==> Successfully installed ucx Fetch: 1.17s. Build: 40.59s. Total: 41.76s. [+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx Input spec -------------------------------- ucx Concretized -------------------------------- ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64 ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64 ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64 ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64 ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64 ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64 ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64 ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64 ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64 ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64 ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64 ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64 ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64 ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64 ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64 ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64 ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64 ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64 ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64 ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64 ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64 ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64 Environment: dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME darwin-fe2.lanl.gov dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq model name : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d -bash: lsb_release: command not found dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date Mon Nov 19 10:47:47 MST 2018 dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd /scratch/users/dantopa/new-spack/pr.ucx.spack Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-11-19new package: mongo-cxx-driver (#9880)Andrea Negri1-0/+18
* new package: mongo-cxx-driver * fixed url
2018-11-19samtools: make zlib/bzip2 dependencies unconditional (#9866)Eric1-2/+2
2018-11-18libmongoc: updated versions (#9877)Andrea Negri1-2/+8
2018-11-18New package: ecFlow, a work flow manager. (#9867)Alberto Chiusole1-0/+30
* New package: ecFlow, a work flow manager. * Fix pep8 style issues.
2018-11-17Add +x variant to petsc. (#9830)Sajid Ali1-1/+9
* modified: var/spack/repos/builtin/packages/petsc/package.py * Update package.py * Update package.py * Update package.py * Update package.py
2018-11-17mixcr: Added a new package for MiXCR. (#9864)simo-tuomisto1-0/+29
* mixcr: Added a new package for MiXCR. * mixcr: Fixed spack license string.
2018-11-16lammps package: added new versions (#9868)Christoph Junghans1-0/+7
2018-11-16py-cython: add new versions (#9846)Sinan1-0/+2
2018-11-16new package: r-gensa (starting at 1.1.7) (#9858)Justin Stanley1-0/+21
2018-11-16py-ply: fix download url (#9862)Eric1-2/+2
2018-11-16vt package: add zlib dependency (#9870)Eric1-0/+2
2018-11-16intel-mkl: fix usage of openmp_libs and tbb_libs (#9863)Denis Davydov1-3/+3
* intel-mkl: fix usage of openmp_libs and tbb_libs * intel-mkl: remove trailing whitespace from openmp lib
2018-11-16r-rgl: update url, add new version (#9796)Levi Baber1-1/+5
2018-11-15py-cffi: add missing pkgconfig dependency (#9784)Michael Kuhn1-0/+1
2018-11-15py-cryptography: add 2.3.1 (#9785)Michael Kuhn1-0/+2
Required for openssl@1.1 compatibility.
2018-11-15krb5: add missing bison dependency for yacc (#9778)Michael Kuhn1-0/+1
2018-11-15globus-toolkit: add missing pkgconfig dependency (#9775)Michael Kuhn1-0/+1
2018-11-15hybpiper: add 1.3.1 (#9762)Justin Stanley0-0/+0
2018-11-15Fix and update verrou (#9847)Hadrien G1-2/+14
* Fix verrou-python integration * Add verrou 2.1.0 * Patch level changed in v2.1.0
2018-11-15dbcsr: minor fixes due to upstream changes (#9799)Denis Davydov1-2/+3
2018-11-15Updated protobuf and py-protobuf to version 3.6.1 (#9536)Leonhard Reichenbach2-2/+5
* Updated protobuf and py-protobuf to version 3.6.1 also updated the download link as the repository has moved * protobuf: modified conflict
2018-11-14Add GMT, CitcomS, and fstrack packages (#9768)Adam J. Stewart8-0/+328
* Add initial packages for citcoms and dependencies * Ignore Pythia imports * Add py-merlin package * Add GMT package * Fixes to get GMT working * Get hc package building * Get CitcomS 3.2.0 working * Add fstrack package * Fix hash
2018-11-14r-cairo: new package (#9794)Levi Baber1-0/+20
* r-cairo: new package * Update var/spack/repos/builtin/packages/r-cairo/package.py Co-Authored-By: baberlevi <baberlevi@gmail.com>
2018-11-14Argobots: added @develop version and +valgrind variant (#9664)dorier1-0/+19
* added develop version in argobots package and added valgrind variant * made autotools required only for develop version * corrected style * Added --disable-valgrind Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
2018-11-14r-phytools: new package at 0.6-60 (#9766)Justin Stanley1-0/+32
* r-phytools: new package at 0.6-60 * r-phytools: add list_url * r-phytools: add deps, dep versions
2018-11-14openblas: add headers property (#9831)Geoffrey Oxberry1-0/+9
This commit adds only the public headers from the full list of headers installed by OpenBLAS; this list of headers is the same as in netlib-lapack.
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